ordisurf {vegan} | R Documentation |
Function ordisurf
fits a smooth surface for given variable and
plots the result on ordination diagram.
ordisurf(x, y, choices=c(1, 2), knots=10, family="gaussian", col="red", thinplate = TRUE, add = FALSE, display = "sites", w = weights(x), main, nlevels = 10, levels, labcex = 0.6, bubble = FALSE, cex = 1, ...)
x |
Ordination configuration, either a matrix or a result known
by scores . |
y |
Variable to be plotted. |
choices |
Ordination axes. |
knots |
Number of initial knots in gam (one
more than degrees of freedom). If knots = 0 or
knots = 1 the function will fit a linear trend surface, and
if knots = 2 the function will fit a quadratic trend surface
instead of a smooth surface. |
family |
Error distribution in gam . |
col |
Colour of contours. |
thinplate |
Use thinplate splines in gam . |
add |
Add contours on an existing diagram or draw a new plot. |
display |
Type of scores known by scores : typically
"sites" for ordinary site scores or "lc" for linear combination scores. |
w |
Prior weights on the data. Concerns mainly cca
and decorana results which have nonconstant weights. |
main |
The main title for the plot, or as default the name of plotted variable in a new plot. |
nlevels, levels |
Either a vector of levels for which contours
are drawn, or suggested number of contours in
nlevels if levels are not supplied. |
labcex |
Label size in contours. Setting this zero will suppress labels. |
bubble |
Use “bubble plot” for points, or vary the point
diameter by the value of the plotted variable. If bubble is
numeric, its value is used for the maximum symbol size (as in
cex ), or if bubble = TRUE , the value of cex gives
the maximum. The minimum size will always be cex = 0.4 . The
option only has an effect if add = FALSE . |
cex |
Character expansion of plotting symbols. |
... |
Other graphical parameters. |
Function ordisurf
fits a smooth surface using thinplate splines
in gam
, and uses predict.gam
to find fitted values in a regular grid.
Function plots the fitted contours with convex hull of data points
either over an existing ordination diagram or draws a new plot
The function uses
scores
to extract ordination scores, and x
can be
any result object known by that function.
User can supply a vector of prior weights w
. If the ordination
object has weights, these will be used. In practise this means that
the row totals are used as weights with
cca
or
decorana
results. If you do not like this, but want to give
equal weights to all sites, you should set w = NULL
. The
behaviour is consistent with envfit
. For complete
accordance with constrained cca
, you should set
display = "lc"
(and possibly scaling = 2
).
Function is usually called for its side effect of drawing the
contour plot. The function returns the result object of class
"ordisurf"
that inherits from gam
used
internally to fit the surface, but adds an item grid
that
contains the data for the grid surface. The item grid
has
elements x
and y
which are vectors of axis coordinates,
and element z
that is a matrix of fitted values for
contour
. The values outside the convex hull of observed
points are NA
in z
. The gam
component of the result can be used for further analysis like
predicting new values (see predict.gam
).
The default is to use thinplate splines. These make sense in ordination as they have equal smoothing in all directions and are rotation invariant.
Dave Roberts and Jari Oksanen
For basic routines gam
,
and scores
. Function
envfit
provides a more traditional and compact
alternative.
data(varespec) data(varechem) library(MASS) vare.dist <- vegdist(varespec) vare.mds <- isoMDS(vare.dist) with(varechem, ordisurf(vare.mds, Baresoil, bubble = 5)) ## Cover of Cladina arbuscula with(varespec, ordisurf(vare.mds, Cla.arb, family=quasipoisson))